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        <ul class="summary" style="margin-left: -15px">
            <li class="chapter" data-level="1.1">
                <ul class="articles">
        <li class="chapter" data-level="1.1.1"  data-name="Basic Tools">
            <b>Basic Tools</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.1.1"  data-name="Copy File to project" title="">
                    <a onclick="openHelp('basic/cp_file.html','1_1_1_1')" href="#"  id="1_1_1_1">Copy File to project</a>
                </li>

                <li class="chapter" data-level="1.1.1.2"  data-name="Link File to project" title="">
                    <a onclick="openHelp('basic/link_file.html','1_1_1_2')" href="#"  id="1_1_1_2">Link File to project</a>
                </li>

                <li class="chapter" data-level="1.1.1.3"  data-name="Convert One of XLS Sheet to tabular txt file" title="()">
                    <a onclick="openHelp('basic/xls2txt.html','1_1_1_3')" href="#"  id="1_1_1_3">Convert One of XLS Sheet to tabular txt file</a>
                </li>

                <li class="chapter" data-level="1.1.1.4"  data-name="Text Format Converts">
                    <a style='color:#52AB6C;'>Text Format Converts</a>
                </li>

                <li class="chapter" data-level="1.1.1.5"  data-name="dos2unix" title="convert Windows/Dos text file to Unix text file">
                    <a onclick="openHelp('dos_unix_convert/dos2unix.html','1_1_1_5')" href="#"  id="1_1_1_5">dos2unix</a>
                </li>

                <li class="chapter" data-level="1.1.1.6"  data-name="unix2dos" title="convert Unix text file to Windows/Dos file">
                    <a onclick="openHelp('dos_unix_convert/unix2dos.html','1_1_1_6')" href="#"  id="1_1_1_6">unix2dos</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.2"  data-name="Text Manipulation">
            <b>Text Manipulation</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.2.7"  data-name="Convert" title="delimiters to TAB">
                    <a onclick="openHelp('textutil/convert_characters.html','1_1_2_7')" href="#"  id="1_1_2_7">Convert</a>
                </li>

                <li class="chapter" data-level="1.1.2.8"  data-name="Concatenate datasets" title="tail-to-head">
                    <a onclick="openHelp('textutil/catWrapper.html','1_1_2_8')" href="#"  id="1_1_2_8">Concatenate datasets</a>
                </li>

                <li class="chapter" data-level="1.1.2.9"  data-name="Cut" title="columns from a table">
                    <a onclick="openHelp('textutil/cutWrapper.html','1_1_2_9')" href="#"  id="1_1_2_9">Cut</a>
                </li>

                <li class="chapter" data-level="1.1.2.10"  data-name="Paste" title="two files side by side">
                    <a onclick="openHelp('textutil/pasteWrapper.html','1_1_2_10')" href="#"  id="1_1_2_10">Paste</a>
                </li>

                <li class="chapter" data-level="1.1.2.11"  data-name="Select first" title="lines from a dataset">
                    <a onclick="openHelp('textutil/headWrapper.html','1_1_2_11')" href="#"  id="1_1_2_11">Select first</a>
                </li>

                <li class="chapter" data-level="1.1.2.12"  data-name="Join, Compare">
                    <a style='color:#52AB6C;'>Join, Compare</a>
                </li>

                <li class="chapter" data-level="1.1.2.13"  data-name="Relational join" title="two datasets a specific column of which has the same value">
                    <a onclick="openHelp('group/joiner2.html','1_1_2_13')" href="#"  id="1_1_2_13">Relational join</a>
                </li>

                <li class="chapter" data-level="1.1.2.14"  data-name="Compare two Datasets" title="to find common or distinct rows">
                    <a onclick="openHelp('group/compare.html','1_1_2_14')" href="#"  id="1_1_2_14">Compare two Datasets</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.3"  data-name="NGS: Fastq/Fasta Tools">
            <b>NGS: Fastq/Fasta Tools</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.3.15"  data-name="Fastq Summary">
                    <a style='color:#52AB6C;'>Fastq Summary</a>
                </li>

                <li class="chapter" data-level="1.1.3.16"  data-name="FASTQ Summary Statistics" title="by column">
                    <a onclick="openHelp('amplicon_seq/fastq_stats.html','1_1_3_16')" href="#"  id="1_1_3_16">FASTQ Summary Statistics</a>
                </li>

                <li class="chapter" data-level="1.1.3.17"  data-name="Draw nucleotides distribution chart" title="from fastq summary statistics file">
                    <a onclick="openHelp('amplicon_seq/fastx_nucleotides_distribution.html','1_1_3_17')" href="#"  id="1_1_3_17">Draw nucleotides distribution chart</a>
                </li>

                <li class="chapter" data-level="1.1.3.18"  data-name="Draw quality score boxplot" title="from fastq summary statistics file">
                    <a onclick="openHelp('amplicon_seq/fastq_quality_boxplot.html','1_1_3_18')" href="#"  id="1_1_3_18">Draw quality score boxplot</a>
                </li>

                <li class="chapter" data-level="1.1.3.19"  data-name="Fastq Quality Control">
                    <a style='color:#52AB6C;'>Fastq Quality Control</a>
                </li>

                <li class="chapter" data-level="1.1.3.20"  data-name="Trimmomatic SE(single-end)" title="flexible read trimming tool for Illumina NGS data">
                    <a onclick="openHelp('amplicon_seq/trimmomatic_se.html','1_1_3_20')" href="#"  id="1_1_3_20">Trimmomatic SE(single-end)</a>
                </li>

                <li class="chapter" data-level="1.1.3.21"  data-name="Trimmomatic PE(paired-end)" title="flexible read trimming tool for Illumina NGS data">
                    <a onclick="openHelp('amplicon_seq/trimmomatic_pe.html','1_1_3_21')" href="#"  id="1_1_3_21">Trimmomatic PE(paired-end)</a>
                </li>

                <li class="chapter" data-level="1.1.3.22"  data-name="Fasta Tools">
                    <a style='color:#52AB6C;'>Fasta Tools</a>
                </li>

                <li class="chapter" data-level="1.1.3.23"  data-name="Convert FASTQ to FASTA" title="">
                    <a onclick="openHelp('amplicon_seq/fastq_to_fasta.html','1_1_3_23')" href="#"  id="1_1_3_23">Convert FASTQ to FASTA</a>
                </li>

                <li class="chapter" data-level="1.1.3.24"  data-name="Compute sequence length" title="for fasta file">
                    <a onclick="openHelp('amplicon_seq/fasta_compute_length.html','1_1_3_24')" href="#"  id="1_1_3_24">Compute sequence length</a>
                </li>

                <li class="chapter" data-level="1.1.3.25"  data-name="Filter sequences by length" title="for fasta file">
                    <a onclick="openHelp('amplicon_seq/fasta_filter_by_length.html','1_1_3_25')" href="#"  id="1_1_3_25">Filter sequences by length</a>
                </li>

                <li class="chapter" data-level="1.1.3.26"  data-name="Fasta Statistics" title="Display summary statistics for a fasta file.">
                    <a onclick="openHelp('amplicon_seq/fasta-stats.html','1_1_3_26')" href="#"  id="1_1_3_26">Fasta Statistics</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.4"  data-name="NGS: Ensembl Files Toolkit">
            <b>NGS: Ensembl Files Toolkit</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.4.27"  data-name="Get GO and KEGG Annotation">
                    <a style='color:#52AB6C;'>Get GO and KEGG Annotation</a>
                </li>

                <li class="chapter" data-level="1.1.4.28"  data-name="Convert Ensembl BioMart GO annotation to VGsoft required format" title="">
                    <a onclick="openHelp('toolkit/go_clean.html','1_1_4_28')" href="#"  id="1_1_4_28">Convert Ensembl BioMart GO annotation to VGsoft required format</a>
                </li>

                <li class="chapter" data-level="1.1.4.29"  data-name="Perform KEGG annotation" title="input protein sequences">
                    <a onclick="openHelp('anno/kegg_anno.html','1_1_4_29')" href="#"  id="1_1_4_29">Perform KEGG annotation</a>
                </li>

                <li class="chapter" data-level="1.1.4.30"  data-name="Preprocess for Quantification Analysis">
                    <a style='color:#52AB6C;'>Preprocess for Quantification Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.4.31"  data-name="Preprocess reference(fasta) and annatation(gtf) from Ensembl" title="">
                    <a onclick="openHelp('cufflinks/gffread_v20190412.html','1_1_4_31')" href="#"  id="1_1_4_31">Preprocess reference(fasta) and annatation(gtf) from Ensembl</a>
                </li>

                <li class="chapter" data-level="1.1.4.32"  data-name="Preprocess cDNA fasta file from Ensembl" title="">
                    <a onclick="openHelp('toolkit/parse_cdna.html','1_1_4_32')" href="#"  id="1_1_4_32">Preprocess cDNA fasta file from Ensembl</a>
                </li>

                <li class="chapter" data-level="1.1.4.33"  data-name="Preprocess protein fasta file from Ensembl" title="for functional annotation">
                    <a onclick="openHelp('toolkit/parse_pep.html','1_1_4_33')" href="#"  id="1_1_4_33">Preprocess protein fasta file from Ensembl</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.5"  data-name="NGS: I. Quantification by Transcript Alignment Based (deprecated)">
            <b>NGS: I. Quantification by Transcript Alignment Based (deprecated)</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.5.34"  data-name="Alignment against Transcripts">
                    <a style='color:#52AB6C;'>Alignment against Transcripts</a>
                </li>

                <li class="chapter" data-level="1.1.5.35"  data-name="Contains:">
                    <a style='color:#52AB6C;'>Contains:</a>
                </li>

                <li class="chapter" data-level="1.1.5.36"  data-name="Build Transcripts Index">
                    <a style='color:#52AB6C;'>Build Transcripts Index</a>
                </li>

                <li class="chapter" data-level="1.1.5.37"  data-name="RSEM and eXpress transcript index" title="">
                    <a onclick="openHelp('exp_cal/rna_ref_build.html','1_1_5_37')" href="#"  id="1_1_5_37">RSEM and eXpress transcript index</a>
                </li>

                <li class="chapter" data-level="1.1.5.38"  data-name="Align and Estimate">
                    <a style='color:#52AB6C;'>Align and Estimate</a>
                </li>

                <li class="chapter" data-level="1.1.5.39"  data-name="RSEM: Align and Estimate Abundance" title="">
                    <a onclick="openHelp('exp_cal/rsem_align_and_estimate_abundance.html','1_1_5_39')" href="#"  id="1_1_5_39">RSEM: Align and Estimate Abundance</a>
                </li>

                <li class="chapter" data-level="1.1.5.40"  data-name="eXpress: Align and Estimate Abundance" title="">
                    <a onclick="openHelp('exp_cal/express_align_and_estimate_abundance.html','1_1_5_40')" href="#"  id="1_1_5_40">eXpress: Align and Estimate Abundance</a>
                </li>

                <li class="chapter" data-level="1.1.5.41"  data-name="Merge Estimates">
                    <a style='color:#52AB6C;'>Merge Estimates</a>
                </li>

                <li class="chapter" data-level="1.1.5.42"  data-name="merge RSEM estimates" title="to matrix">
                    <a onclick="openHelp('rna_utils/rsem_abundance_estimates_to_matrix.html','1_1_5_42')" href="#"  id="1_1_5_42">merge RSEM estimates</a>
                </li>

                <li class="chapter" data-level="1.1.5.43"  data-name="merge eXpress estimates" title="to matrix">
                    <a onclick="openHelp('rna_utils/express_abundance_estimates_to_matrix.html','1_1_5_43')" href="#"  id="1_1_5_43">merge eXpress estimates</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.6"  data-name="NGS: II. Quantification by Transcript Alignment Free">
            <b>NGS: II. Quantification by Transcript Alignment Free</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.6.44"  data-name="Alignment Free">
                    <a style='color:#52AB6C;'>Alignment Free</a>
                </li>

                <li class="chapter" data-level="1.1.6.45"  data-name="Contains:">
                    <a style='color:#52AB6C;'>Contains:</a>
                </li>

                <li class="chapter" data-level="1.1.6.46"  data-name="Build Transcripts Index">
                    <a style='color:#52AB6C;'>Build Transcripts Index</a>
                </li>

                <li class="chapter" data-level="1.1.6.47"  data-name="Kallisto transcript index" title="- build transcript index">
                    <a onclick="openHelp('kallisto/kallisto_index.html','1_1_6_47')" href="#"  id="1_1_6_47">Kallisto transcript index</a>
                </li>

                <li class="chapter" data-level="1.1.6.48"  data-name="Estimate">
                    <a style='color:#52AB6C;'>Estimate</a>
                </li>

                <li class="chapter" data-level="1.1.6.49"  data-name="Kallisto quant" title="- quantify abundances of RNA-Seq transcripts">
                    <a onclick="openHelp('kallisto/kallisto_quant.html','1_1_6_49')" href="#"  id="1_1_6_49">Kallisto quant</a>
                </li>

                <li class="chapter" data-level="1.1.6.50"  data-name="Merge Estimates">
                    <a style='color:#52AB6C;'>Merge Estimates</a>
                </li>

                <li class="chapter" data-level="1.1.6.51"  data-name="merge Kallisto estimates" title="to matrix">
                    <a onclick="openHelp('kallisto/kallisto_abundance_estimates_to_matrix.html','1_1_6_51')" href="#"  id="1_1_6_51">merge Kallisto estimates</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.7"  data-name="NGS: III. Quantification by Genome Alignment">
            <b>NGS: III. Quantification by Genome Alignment</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.7.52"  data-name="Alignment against Genome">
                    <a style='color:#52AB6C;'>Alignment against Genome</a>
                </li>

                <li class="chapter" data-level="1.1.7.53"  data-name="Contains:">
                    <a style='color:#52AB6C;'>Contains:</a>
                </li>

                <li class="chapter" data-level="1.1.7.54"  data-name="Build Genome Index">
                    <a style='color:#52AB6C;'>Build Genome Index</a>
                </li>

                <li class="chapter" data-level="1.1.7.55"  data-name="HISAT2 reference index" title="()">
                    <a onclick="openHelp('hisat2_mapper/hisat2_ref_build.html','1_1_7_55')" href="#"  id="1_1_7_55">HISAT2 reference index</a>
                </li>

                <li class="chapter" data-level="1.1.7.56"  data-name="Spliced Aligner">
                    <a style='color:#52AB6C;'>Spliced Aligner</a>
                </li>

                <li class="chapter" data-level="1.1.7.57"  data-name="HISAT2" title="A fast and sensitive alignment program">
                    <a onclick="openHelp('hisat2_mapper/hisat2.html','1_1_7_57')" href="#"  id="1_1_7_57">HISAT2</a>
                </li>

                <li class="chapter" data-level="1.1.7.58"  data-name="Estimate">
                    <a style='color:#52AB6C;'>Estimate</a>
                </li>

                <li class="chapter" data-level="1.1.7.59"  data-name="Cuffquant" title="Precompute gene expression levels">
                    <a onclick="openHelp('cufflinks/cuffquant.html','1_1_7_59')" href="#"  id="1_1_7_59">Cuffquant</a>
                </li>

                <li class="chapter" data-level="1.1.7.60"  data-name="Cuffnorm" title="Create normalized expression levels">
                    <a onclick="openHelp('cufflinks/cuffnorm.html','1_1_7_60')" href="#"  id="1_1_7_60">Cuffnorm</a>
                </li>

                <li class="chapter" data-level="1.1.7.61"  data-name="DE By Cuffdiff">
                    <a style='color:#52AB6C;'>DE By Cuffdiff</a>
                </li>

                <li class="chapter" data-level="1.1.7.62"  data-name="Cuffdiff" title="find significant changes in transcript/gene expression">
                    <a onclick="openHelp('cufflinks/cuffdiff.html','1_1_7_62')" href="#"  id="1_1_7_62">Cuffdiff</a>
                </li>

                <li class="chapter" data-level="1.1.7.63"  data-name="Parse Cuffdiff results" title="split and plot among comparisons">
                    <a onclick="openHelp('cufflinks/parse_cuffdiff.html','1_1_7_63')" href="#"  id="1_1_7_63">Parse Cuffdiff results</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.8"  data-name="NGS: RNA-Seq Quality Control">
            <b>NGS: RNA-Seq Quality Control</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.8.64"  data-name="Gene Body Coverage (BAM)" title="Read coverage over gene body.">
                    <a onclick="openHelp('RSeQC/geneBody_coverage.html','1_1_8_64')" href="#"  id="1_1_8_64">Gene Body Coverage (BAM)</a>
                </li>

                <li class="chapter" data-level="1.1.8.65"  data-name="RPKM Saturation" title="calculates raw count and RPKM values for transcript at exon, intron, and mRNA level">
                    <a onclick="openHelp('RSeQC/RPKM_saturation.html','1_1_8_65')" href="#"  id="1_1_8_65">RPKM Saturation</a>
                </li>

                <li class="chapter" data-level="1.1.8.66"  data-name="Read Distribution" title="calculates how mapped reads were distributed over genome feature">
                    <a onclick="openHelp('RSeQC/read_distribution.html','1_1_8_66')" href="#"  id="1_1_8_66">Read Distribution</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.9"  data-name="NGS: RNA Assembly &amp; AS Analysis">
            <b>NGS: RNA Assembly &amp; AS Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.9.67"  data-name="Knowledge-based Assembly">
                    <a style='color:#52AB6C;'>Knowledge-based Assembly</a>
                </li>

                <li class="chapter" data-level="1.1.9.68"  data-name="Cufflinks" title="transcript assembly and FPKM (RPKM) estimates for RNA-Seq data">
                    <a onclick="openHelp('cufflinks/cufflinks.html','1_1_9_68')" href="#"  id="1_1_9_68">Cufflinks</a>
                </li>

                <li class="chapter" data-level="1.1.9.69"  data-name="New Transcripts">
                    <a style='color:#52AB6C;'>New Transcripts</a>
                </li>

                <li class="chapter" data-level="1.1.9.70"  data-name="Cuffcompare" title="compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments">
                    <a onclick="openHelp('cufflinks/cuffcompare.html','1_1_9_70')" href="#"  id="1_1_9_70">Cuffcompare</a>
                </li>

                <li class="chapter" data-level="1.1.9.71"  data-name="Cuffmerge" title="merge together several Cufflinks assemblies">
                    <a onclick="openHelp('cufflinks/cuffmerge.html','1_1_9_71')" href="#"  id="1_1_9_71">Cuffmerge</a>
                </li>

                <li class="chapter" data-level="1.1.9.72"  data-name="Filter Cuffcompare output GTF" title="according to Transfrag class code">
                    <a onclick="openHelp('cufflinks/filter_cuffcmp_gtf.html','1_1_9_72')" href="#"  id="1_1_9_72">Filter Cuffcompare output GTF</a>
                </li>

                <li class="chapter" data-level="1.1.9.73"  data-name="Alternative Splicing">
                    <a style='color:#52AB6C;'>Alternative Splicing</a>
                </li>

                <li class="chapter" data-level="1.1.9.74"  data-name="ASprofile" title="extract AS events from GTF, such as that created by Cufflinks">
                    <a onclick="openHelp('ASprofile/as_analysis.html','1_1_9_74')" href="#"  id="1_1_9_74">ASprofile</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.10"  data-name="NGS: Call SNPs &amp; InDels">
            <b>NGS: Call SNPs &amp; InDels</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.10.75"  data-name="BWA -> GATK Pipeline">
                    <a style='color:#52AB6C;'>BWA -> GATK Pipeline</a>
                </li>

                <li class="chapter" data-level="1.1.10.76"  data-name="Contains">
                    <a style='color:#52AB6C;'>Contains</a>
                </li>

                <li class="chapter" data-level="1.1.10.77"  data-name="Build Reference Index">
                    <a style='color:#52AB6C;'>Build Reference Index</a>
                </li>

                <li class="chapter" data-level="1.1.10.78"  data-name="BWA reference index" title="()">
                    <a onclick="openHelp('bwa_mapping/bwa_ref_build.html','1_1_10_78')" href="#"  id="1_1_10_78">BWA reference index</a>
                </li>

                <li class="chapter" data-level="1.1.10.79"  data-name="BWA Mapping">
                    <a style='color:#52AB6C;'>BWA Mapping</a>
                </li>

                <li class="chapter" data-level="1.1.10.80"  data-name="Map with BWA" title="- map short reads (&lt; 100 bp) against reference genome">
                    <a onclick="openHelp('bwa_mapping/bwa.html','1_1_10_80')" href="#"  id="1_1_10_80">Map with BWA</a>
                </li>

                <li class="chapter" data-level="1.1.10.81"  data-name="Map with BWA-MEM" title="- map medium and long reads (&gt; 100 bp) against reference genome">
                    <a onclick="openHelp('bwa_mapping/bwa-mem.html','1_1_10_81')" href="#"  id="1_1_10_81">Map with BWA-MEM</a>
                </li>

                <li class="chapter" data-level="1.1.10.82"  data-name="SNPs/InDels Caller">
                    <a style='color:#52AB6C;'>SNPs/InDels Caller</a>
                </li>

                <li class="chapter" data-level="1.1.10.83"  data-name="GATK Unified Genotyper" title="()">
                    <a onclick="openHelp('varient_calling/unified_genotyper.html','1_1_10_83')" href="#"  id="1_1_10_83">GATK Unified Genotyper</a>
                </li>

                <li class="chapter" data-level="1.1.10.84"  data-name="VCF Filters">
                    <a style='color:#52AB6C;'>VCF Filters</a>
                </li>

                <li class="chapter" data-level="1.1.10.85"  data-name="Filter VCF File" title="according to variant quality etc.">
                    <a onclick="openHelp('varient_calling/myVcfUtils.html','1_1_10_85')" href="#"  id="1_1_10_85">Filter VCF File</a>
                </li>

                <li class="chapter" data-level="1.1.10.86"  data-name="VCF Stat">
                    <a style='color:#52AB6C;'>VCF Stat</a>
                </li>

                <li class="chapter" data-level="1.1.10.87"  data-name="Statistics Variation Information" title="from vcf file">
                    <a onclick="openHelp('varient_calling/stat_variation.html','1_1_10_87')" href="#"  id="1_1_10_87">Statistics Variation Information</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.11"  data-name="NGS: BAM/SAM Tools">
            <b>NGS: BAM/SAM Tools</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.11.88"  data-name="Converts">
                    <a style='color:#52AB6C;'>Converts</a>
                </li>

                <li class="chapter" data-level="1.1.11.89"  data-name="SAM-to-BAM" title="convert SAM to BAM">
                    <a onclick="openHelp('bam_sam_tools/sam_to_bam.html','1_1_11_89')" href="#"  id="1_1_11_89">SAM-to-BAM</a>
                </li>

                <li class="chapter" data-level="1.1.11.90"  data-name="BAM-to-SAM" title="convert BAM to SAM">
                    <a onclick="openHelp('bam_sam_tools/bam_to_sam.html','1_1_11_90')" href="#"  id="1_1_11_90">BAM-to-SAM</a>
                </li>

                <li class="chapter" data-level="1.1.11.91"  data-name="Utils">
                    <a style='color:#52AB6C;'>Utils</a>
                </li>

                <li class="chapter" data-level="1.1.11.92"  data-name="Filter BAM" title="file on MAPQ or by region">
                    <a onclick="openHelp('bam_sam_tools/samtool_filter2.html','1_1_11_92')" href="#"  id="1_1_11_92">Filter BAM</a>
                </li>

                <li class="chapter" data-level="1.1.11.93"  data-name="Sort BAM" title="dataset">
                    <a onclick="openHelp('bam_sam_tools/samtools_sort.html','1_1_11_93')" href="#"  id="1_1_11_93">Sort BAM</a>
                </li>

                <li class="chapter" data-level="1.1.11.94"  data-name="BAM Flagstat" title="tabulate descriptive stats for BAM datset">
                    <a onclick="openHelp('bam_sam_tools/samtools_flagstat.html','1_1_11_94')" href="#"  id="1_1_11_94">BAM Flagstat</a>
                </li>

                <li class="chapter" data-level="1.1.11.95"  data-name="BAM IdxStats" title="tabulate mapping statistics for BAM dataset">
                    <a onclick="openHelp('bam_sam_tools/samtools_idxstats.html','1_1_11_95')" href="#"  id="1_1_11_95">BAM IdxStats</a>
                </li>

                <li class="chapter" data-level="1.1.11.96"  data-name="BAM RmDup" title="remove PCR duplicates">
                    <a onclick="openHelp('bam_sam_tools/samtools_rmdup.html','1_1_11_96')" href="#"  id="1_1_11_96">BAM RmDup</a>
                </li>

                <li class="chapter" data-level="1.1.11.97"  data-name="Merge sorted BAM Files" title="merges sorted BAM files together">
                    <a onclick="openHelp('bam_sam_tools/sam_merge.html','1_1_11_97')" href="#"  id="1_1_11_97">Merge sorted BAM Files</a>
                </li>

                <li class="chapter" data-level="1.1.11.98"  data-name="Region Depth Coverage">
                    <a style='color:#52AB6C;'>Region Depth Coverage</a>
                </li>

                <li class="chapter" data-level="1.1.11.99"  data-name="read depth per BED region" title="calculate read depth for a set of genomic intervals">
                    <a onclick="openHelp('bam_sam_tools/samtools_bedcov.html','1_1_11_99')" href="#"  id="1_1_11_99">read depth per BED region</a>
                </li>

                <li class="chapter" data-level="1.1.11.100"  data-name="read coverage per BED region" title="calculate read coverage for a set of genomic intervals">
                    <a onclick="openHelp('bam_sam_tools/coverageBed.html','1_1_11_100')" href="#"  id="1_1_11_100">read coverage per BED region</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.12"  data-name="NGS: FPKM/TPM Normalization">
            <b>NGS: FPKM/TPM Normalization</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.12.101"  data-name="Gene/Transcript Length">
                    <a style='color:#52AB6C;'>Gene/Transcript Length</a>
                </li>

                <li class="chapter" data-level="1.1.12.102"  data-name="Get gene and isoform length from gtf file" title="">
                    <a onclick="openHelp('normalize/gtf_glength.html','1_1_12_102')" href="#"  id="1_1_12_102">Get gene and isoform length from gtf file</a>
                </li>

                <li class="chapter" data-level="1.1.12.103"  data-name="Get gene and isoform length from transcripts fasta file" title="">
                    <a onclick="openHelp('normalize/cds_glength.html','1_1_12_103')" href="#"  id="1_1_12_103">Get gene and isoform length from transcripts fasta file</a>
                </li>

                <li class="chapter" data-level="1.1.12.104"  data-name="Normalization: TPM recommended ">
                    <a style='color:#52AB6C;'>Normalization: TPM recommended </a>
                </li>

                <li class="chapter" data-level="1.1.12.105"  data-name="FPKM normalization" title="Convert count matrix to FPKM matrix">
                    <a onclick="openHelp('normalize/count2fpkm.html','1_1_12_105')" href="#"  id="1_1_12_105">FPKM normalization</a>
                </li>

                <li class="chapter" data-level="1.1.12.106"  data-name="TPM normalization" title="Convert count matrix to TPM matrix">
                    <a onclick="openHelp('normalize/count2tpm.html','1_1_12_106')" href="#"  id="1_1_12_106">TPM normalization</a>
                </li>

                <li class="chapter" data-level="1.1.12.107"  data-name="TMM scaling and FPKM normalization" title="on count matrix">
                    <a onclick="openHelp('rnaseq_toolkit/TMM_normalization.html','1_1_12_107')" href="#"  id="1_1_12_107">TMM scaling and FPKM normalization</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.13"  data-name="NGS: Matrix Operations">
            <b>NGS: Matrix Operations</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.13.108"  data-name="Utils">
                    <a style='color:#52AB6C;'>Utils</a>
                </li>

                <li class="chapter" data-level="1.1.13.109"  data-name="Fetch all genes(row names) list from matrix" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/fetch_all_genes.html','1_1_13_109')" href="#"  id="1_1_13_109">Fetch all genes(row names) list from matrix</a>
                </li>

                <li class="chapter" data-level="1.1.13.110"  data-name="Retrieve Rows from matrix/tabular file" title="using genes/identifiers list file">
                    <a onclick="openHelp('rnaseq_toolkit/retri_rows.html','1_1_13_110')" href="#"  id="1_1_13_110">Retrieve Rows from matrix/tabular file</a>
                </li>

                <li class="chapter" data-level="1.1.13.111"  data-name="Transformation">
                    <a style='color:#52AB6C;'>Transformation</a>
                </li>

                <li class="chapter" data-level="1.1.13.112"  data-name="FPKM/TPM matrix log2 transform" title="">
                    <a onclick="openHelp('rnaseq_toolkit/log2_transform.html','1_1_13_112')" href="#"  id="1_1_13_112">FPKM/TPM matrix log2 transform</a>
                </li>

                <li class="chapter" data-level="1.1.13.113"  data-name="Replicates to Sample averages" title="for fpkm/tpm matrix">
                    <a onclick="openHelp('rnaseq_toolkit/replicates_to_sample_averages_matrix.html','1_1_13_113')" href="#"  id="1_1_13_113">Replicates to Sample averages</a>
                </li>

                <li class="chapter" data-level="1.1.13.114"  data-name="Matrix Transpose" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/matrix_transpose.html','1_1_13_114')" href="#"  id="1_1_13_114">Matrix Transpose</a>
                </li>

                <li class="chapter" data-level="1.1.13.115"  data-name="Merge and Reorder">
                    <a style='color:#52AB6C;'>Merge and Reorder</a>
                </li>

                <li class="chapter" data-level="1.1.13.116"  data-name="Merge Matrices" title="like, fpkm/tpm/count matrix etc.">
                    <a onclick="openHelp('rnaseq_toolkit/merge_matrices.html','1_1_13_116')" href="#"  id="1_1_13_116">Merge Matrices</a>
                </li>

                <li class="chapter" data-level="1.1.13.117"  data-name="Reorder Matrix columns" title="according to a sample name list file">
                    <a onclick="openHelp('rnaseq_toolkit/reorder_sample.html','1_1_13_117')" href="#"  id="1_1_13_117">Reorder Matrix columns</a>
                </li>

                <li class="chapter" data-level="1.1.13.118"  data-name="Sub-Matrix">
                    <a style='color:#52AB6C;'>Sub-Matrix</a>
                </li>

                <li class="chapter" data-level="1.1.13.119"  data-name="Get a sub-Matrix" title="using samples defined in sample group design file">
                    <a onclick="openHelp('rnaseq_toolkit/subOTU_table.html','1_1_13_119')" href="#"  id="1_1_13_119">Get a sub-Matrix</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.14"  data-name="NGS: RNA-Seq DE Analysis">
            <b>NGS: RNA-Seq DE Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.14.120"  data-name="Differential Expression Analysis">
                    <a style='color:#52AB6C;'>Differential Expression Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.14.121"  data-name="Differential Expression Analysis" title="Identify differentially expressed results Using EdgeR,DESeq2,limma">
                    <a onclick="openHelp('rnaseq_toolkit/diffExpress.html','1_1_14_121')" href="#"  id="1_1_14_121">Differential Expression Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.14.122"  data-name="Filter and Summary">
                    <a style='color:#52AB6C;'>Filter and Summary</a>
                </li>

                <li class="chapter" data-level="1.1.14.123"  data-name="Filter DE Analysis Result" title="according to pval, FDR/padj, logfc">
                    <a onclick="openHelp('rnaseq_toolkit/filter_diff_expr.html','1_1_14_123')" href="#"  id="1_1_14_123">Filter DE Analysis Result</a>
                </li>

                <li class="chapter" data-level="1.1.14.124"  data-name="Summary DE Analysis Result" title="set pval, FDR/padj, logfc cutoff">
                    <a onclick="openHelp('rnaseq_toolkit/summary_DE.html','1_1_14_124')" href="#"  id="1_1_14_124">Summary DE Analysis Result</a>
                </li>

                <li class="chapter" data-level="1.1.14.125"  data-name="Utils">
                    <a style='color:#52AB6C;'>Utils</a>
                </li>

                <li class="chapter" data-level="1.1.14.126"  data-name="Generate sample group file from file header" title="like Matrix file header etc.">
                    <a onclick="openHelp('rnaseq_toolkit/ge_sample_group2.html','1_1_14_126')" href="#"  id="1_1_14_126">Generate sample group file from file header</a>
                </li>

                <li class="chapter" data-level="1.1.14.127"  data-name="Retrieve All Diff Genes list" title="from filtered DE result html file">
                    <a onclick="openHelp('rnaseq_toolkit/get_diff_geneList.html','1_1_14_127')" href="#"  id="1_1_14_127">Retrieve All Diff Genes list</a>
                </li>

                <li class="chapter" data-level="1.1.14.128"  data-name="Batch Tools">
                    <a style='color:#52AB6C;'>Batch Tools</a>
                </li>

                <li class="chapter" data-level="1.1.14.129"  data-name="Batch Mode: Filter DE Analysis Result" title="according to pval, FDR/padj, logfc">
                    <a onclick="openHelp('rnaseq_toolkit/batch_filter_diff_expr.html','1_1_14_129')" href="#"  id="1_1_14_129">Batch Mode: Filter DE Analysis Result</a>
                </li>

                <li class="chapter" data-level="1.1.14.130"  data-name="Batch Mode: Retrieve Diff Genes list" title="from filtered DE html result or subcluster analysis html result">
                    <a onclick="openHelp('rnaseq_toolkit/batch_get_diff_geneList.html','1_1_14_130')" href="#"  id="1_1_14_130">Batch Mode: Retrieve Diff Genes list</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.15"  data-name="NGS: RNA-Seq Analysis Toolkits">
            <b>NGS: RNA-Seq Analysis Toolkits</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.15.131"  data-name="PCA and PCOA">
                    <a style='color:#52AB6C;'>PCA and PCOA</a>
                </li>

                <li class="chapter" data-level="1.1.15.132"  data-name="PCA analysis and plot PCA" title="with fpkm/tpm matrix">
                    <a onclick="openHelp('rnaseq_toolkit/plot-pca.html','1_1_15_132')" href="#"  id="1_1_15_132">PCA analysis and plot PCA</a>
                </li>

                <li class="chapter" data-level="1.1.15.133"  data-name="PCOA analysis and plot PCOA" title="from distance matrix">
                    <a onclick="openHelp('rnaseq_toolkit/plot-pcoa.html','1_1_15_133')" href="#"  id="1_1_15_133">PCOA analysis and plot PCOA</a>
                </li>

                <li class="chapter" data-level="1.1.15.134"  data-name="3D Scatterplot" title="for PCA/PCOA analysis result">
                    <a onclick="openHelp('rnaseq_toolkit/scatterplot3d.html','1_1_15_134')" href="#"  id="1_1_15_134">3D Scatterplot</a>
                </li>

                <li class="chapter" data-level="1.1.15.135"  data-name="Correlation and Distance">
                    <a style='color:#52AB6C;'>Correlation and Distance</a>
                </li>

                <li class="chapter" data-level="1.1.15.136"  data-name="Create Sample Correlation Matrix" title="and make heatmap plot">
                    <a onclick="openHelp('rnaseq_toolkit/sample_cor_matrix.html','1_1_15_136')" href="#"  id="1_1_15_136">Create Sample Correlation Matrix</a>
                </li>

                <li class="chapter" data-level="1.1.15.137"  data-name="Generate distance matrix" title="from fpkm/tpm matrix">
                    <a onclick="openHelp('rnaseq_toolkit/make_dist.html','1_1_15_137')" href="#"  id="1_1_15_137">Generate distance matrix</a>
                </li>

                <li class="chapter" data-level="1.1.15.138"  data-name="Make Distance HeatMap" title="from distance matrix">
                    <a onclick="openHelp('rnaseq_toolkit/plot-dist.html','1_1_15_138')" href="#"  id="1_1_15_138">Make Distance HeatMap</a>
                </li>

                <li class="chapter" data-level="1.1.15.139"  data-name="Make Distance Boxplots" title="given a Sample Group information">
                    <a onclick="openHelp('rnaseq_toolkit/make_distance_boxplots.html','1_1_15_139')" href="#"  id="1_1_15_139">Make Distance Boxplots</a>
                </li>

                <li class="chapter" data-level="1.1.15.140"  data-name="Make Density Plot" title="from all values in Distance/Correlation_coefficient matrix">
                    <a onclick="openHelp('rnaseq_toolkit/dist_hist_plot.html','1_1_15_140')" href="#"  id="1_1_15_140">Make Density Plot</a>
                </li>

                <li class="chapter" data-level="1.1.15.141"  data-name="Heatmap and Hclust Tree">
                    <a style='color:#52AB6C;'>Heatmap and Hclust Tree</a>
                </li>

                <li class="chapter" data-level="1.1.15.142"  data-name="Plot heatmap with tree" title="for fpkm/tpm matrix data">
                    <a onclick="openHelp('rnaseq_toolkit/heatmap.html','1_1_15_142')" href="#"  id="1_1_15_142">Plot heatmap with tree</a>
                </li>

                <li class="chapter" data-level="1.1.15.143"  data-name="Plot hcluster tree" title="input a fpkm/tpm matrix">
                    <a onclick="openHelp('rnaseq_toolkit/hcluster_tree.html','1_1_15_143')" href="#"  id="1_1_15_143">Plot hcluster tree</a>
                </li>

                <li class="chapter" data-level="1.1.15.144"  data-name="Plot Tree" title="using Newick tree format file">
                    <a onclick="openHelp('rnaseq_toolkit/plot-tree.html','1_1_15_144')" href="#"  id="1_1_15_144">Plot Tree</a>
                </li>

                <li class="chapter" data-level="1.1.15.145"  data-name="Visualized Analysis">
                    <a style='color:#52AB6C;'>Visualized Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.15.146"  data-name="Plot FPKM/TPM distribution for all samples" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/plot_fpkm_dist.html','1_1_15_146')" href="#"  id="1_1_15_146">Plot FPKM/TPM distribution for all samples</a>
                </li>

                <li class="chapter" data-level="1.1.15.147"  data-name="FPKM/TPM Boxplot for all samples" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/boxplots.html','1_1_15_147')" href="#"  id="1_1_15_147">FPKM/TPM Boxplot for all samples</a>
                </li>

                <li class="chapter" data-level="1.1.15.148"  data-name="FPKM/TPM Scatterplot for two samples" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/fpkm_scatterplot.html','1_1_15_148')" href="#"  id="1_1_15_148">FPKM/TPM Scatterplot for two samples</a>
                </li>

                <li class="chapter" data-level="1.1.15.149"  data-name="FPKM/TPM Scatterplot for all pair-wise samples" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/pair_wise_scatterplot.html','1_1_15_149')" href="#"  id="1_1_15_149">FPKM/TPM Scatterplot for all pair-wise samples</a>
                </li>

                <li class="chapter" data-level="1.1.15.150"  data-name="Matrix to gene plots" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/matrix_to_gene_plots.html','1_1_15_150')" href="#"  id="1_1_15_150">Matrix to gene plots</a>
                </li>

                <li class="chapter" data-level="1.1.15.151"  data-name="Plot Venn Diagram" title="from genes list files">
                    <a onclick="openHelp('rnaseq_toolkit/venn.html','1_1_15_151')" href="#"  id="1_1_15_151">Plot Venn Diagram</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.16"  data-name="NGS: GO Analysis">
            <b>NGS: GO Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.16.152"  data-name="Utils">
                    <a style='color:#52AB6C;'>Utils</a>
                </li>

                <li class="chapter" data-level="1.1.16.153"  data-name="Add GO Annotation" title="to DE results file">
                    <a onclick="openHelp('rnaseq_toolkit/add_go_anno.html','1_1_16_153')" href="#"  id="1_1_16_153">Add GO Annotation</a>
                </li>

                <li class="chapter" data-level="1.1.16.154"  data-name="GO level statistic about GO annotation file" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/gene_ontology.html','1_1_16_154')" href="#"  id="1_1_16_154">GO level statistic about GO annotation file</a>
                </li>

                <li class="chapter" data-level="1.1.16.155"  data-name="Plot GO bar" title="from GO level stat file">
                    <a onclick="openHelp('rnaseq_toolkit/go-bar.html','1_1_16_155')" href="#"  id="1_1_16_155">Plot GO bar</a>
                </li>

                <li class="chapter" data-level="1.1.16.156"  data-name="Report all input Gene->GO Relations" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/report_genes2GO.html','1_1_16_156')" href="#"  id="1_1_16_156">Report all input Gene->GO Relations</a>
                </li>

                <li class="chapter" data-level="1.1.16.157"  data-name="Print the hierarchy below GO Term" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/write_hierarchy.html','1_1_16_157')" href="#"  id="1_1_16_157">Print the hierarchy below GO Term</a>
                </li>

                <li class="chapter" data-level="1.1.16.158"  data-name="Enrichment">
                    <a style='color:#52AB6C;'>Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.16.159"  data-name="GO Enrichment Analysis" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/find_enrichment.html','1_1_16_159')" href="#"  id="1_1_16_159">GO Enrichment Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.16.160"  data-name="Plot GO Enrichment" title="from GO enrich result">
                    <a onclick="openHelp('rnaseq_toolkit/go_enrich_plot.html','1_1_16_160')" href="#"  id="1_1_16_160">Plot GO Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.16.161"  data-name="GO Enrichment Bar Plot" title="from GO enrich result">
                    <a onclick="openHelp('rnaseq_toolkit/go_enrich_barplot.html','1_1_16_161')" href="#"  id="1_1_16_161">GO Enrichment Bar Plot</a>
                </li>

                <li class="chapter" data-level="1.1.16.162"  data-name="Summary GO Enrichment" title="from multiple GO Enrichment results">
                    <a onclick="openHelp('rnaseq_toolkit/go_stat.html','1_1_16_162')" href="#"  id="1_1_16_162">Summary GO Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.16.163"  data-name="Graph">
                    <a style='color:#52AB6C;'>Graph</a>
                </li>

                <li class="chapter" data-level="1.1.16.164"  data-name="Plot Enriched GO DAG Grapth" title="from GO enrichment result">
                    <a onclick="openHelp('rnaseq_toolkit/enrich_go_dag.html','1_1_16_164')" href="#"  id="1_1_16_164">Plot Enriched GO DAG Grapth</a>
                </li>

                <li class="chapter" data-level="1.1.16.165"  data-name="Plot GO lineage DAG Grapth" title="from a GOs file">
                    <a onclick="openHelp('rnaseq_toolkit/plot_go_term.html','1_1_16_165')" href="#"  id="1_1_16_165">Plot GO lineage DAG Grapth</a>
                </li>

                <li class="chapter" data-level="1.1.16.166"  data-name="Plot GO lineage DAG Grapth with Pvalue" title="from a GOs and Pvalues file">
                    <a onclick="openHelp('rnaseq_toolkit/plot_go_term2.html','1_1_16_166')" href="#"  id="1_1_16_166">Plot GO lineage DAG Grapth with Pvalue</a>
                </li>

                <li class="chapter" data-level="1.1.16.167"  data-name="Batch Tools">
                    <a style='color:#52AB6C;'>Batch Tools</a>
                </li>

                <li class="chapter" data-level="1.1.16.168"  data-name="Batch Mode: Add GO Annotation" title="to DE results file">
                    <a onclick="openHelp('rnaseq_toolkit/batch_add_go_anno.html','1_1_16_168')" href="#"  id="1_1_16_168">Batch Mode: Add GO Annotation</a>
                </li>

                <li class="chapter" data-level="1.1.16.169"  data-name="Batch Mode: GO Enrichment Analysis" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/batch_find_enrichment.html','1_1_16_169')" href="#"  id="1_1_16_169">Batch Mode: GO Enrichment Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.16.170"  data-name="Batch Mode: Plot GO Enrichment" title="from GO enrich html result">
                    <a onclick="openHelp('rnaseq_toolkit/batch_go_enrich_plot.html','1_1_16_170')" href="#"  id="1_1_16_170">Batch Mode: Plot GO Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.16.171"  data-name="Batch Mode: GO Enrichment Bar Plot" title="from GO enrich html result">
                    <a onclick="openHelp('rnaseq_toolkit/batch_go_enrich_barplot.html','1_1_16_171')" href="#"  id="1_1_16_171">Batch Mode: GO Enrichment Bar Plot</a>
                </li>

                <li class="chapter" data-level="1.1.16.172"  data-name="Batch Mode: Plot Enriched GO DAG Grapth" title="from GO enrichment html result">
                    <a onclick="openHelp('rnaseq_toolkit/batch_enrich_go_dag.html','1_1_16_172')" href="#"  id="1_1_16_172">Batch Mode: Plot Enriched GO DAG Grapth</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.17"  data-name="NGS: KEGG Analysis">
            <b>NGS: KEGG Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.17.173"  data-name="Utils">
                    <a style='color:#52AB6C;'>Utils</a>
                </li>

                <li class="chapter" data-level="1.1.17.174"  data-name="Add KEGG Annotation" title="to DE results file">
                    <a onclick="openHelp('rnaseq_toolkit/add_kegg_anno.html','1_1_17_174')" href="#"  id="1_1_17_174">Add KEGG Annotation</a>
                </li>

                <li class="chapter" data-level="1.1.17.175"  data-name="KEGG statistic about KEGG annotation file" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/kegg_anno_stat.html','1_1_17_175')" href="#"  id="1_1_17_175">KEGG statistic about KEGG annotation file</a>
                </li>

                <li class="chapter" data-level="1.1.17.176"  data-name="Enrichment">
                    <a style='color:#52AB6C;'>Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.17.177"  data-name="KEGG Enrichment Analysis" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/identify.html','1_1_17_177')" href="#"  id="1_1_17_177">KEGG Enrichment Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.17.178"  data-name="Plot KEGG Enrichment" title="from KEGG enrich result">
                    <a onclick="openHelp('rnaseq_toolkit/kegg_enrich_plot.html','1_1_17_178')" href="#"  id="1_1_17_178">Plot KEGG Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.17.179"  data-name="Summary KEGG Enrichment" title="from multiple KEGG Enrichment results">
                    <a onclick="openHelp('rnaseq_toolkit/kegg_stat.html','1_1_17_179')" href="#"  id="1_1_17_179">Summary KEGG Enrichment</a>
                </li>

                <li class="chapter" data-level="1.1.17.180"  data-name="Batch Tools">
                    <a style='color:#52AB6C;'>Batch Tools</a>
                </li>

                <li class="chapter" data-level="1.1.17.181"  data-name="Batch Mode: Add KEGG Annotation" title="to DE results file">
                    <a onclick="openHelp('rnaseq_toolkit/batch_add_kegg_anno.html','1_1_17_181')" href="#"  id="1_1_17_181">Batch Mode: Add KEGG Annotation</a>
                </li>

                <li class="chapter" data-level="1.1.17.182"  data-name="Batch Mode: KEGG Enrichment Analysis" title="()">
                    <a onclick="openHelp('rnaseq_toolkit/batch_identify.html','1_1_17_182')" href="#"  id="1_1_17_182">Batch Mode: KEGG Enrichment Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.17.183"  data-name="Batch Mode: Plot KEGG Enrichment" title="from KEGG enrich html result">
                    <a onclick="openHelp('rnaseq_toolkit/batch_kegg_enrich_plot.html','1_1_17_183')" href="#"  id="1_1_17_183">Batch Mode: Plot KEGG Enrichment</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.18"  data-name="NGS: WGCNA Analysis">
            <b>NGS: WGCNA Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.18.184"  data-name="Preprocess">
                    <a style='color:#52AB6C;'>Preprocess</a>
                </li>

                <li class="chapter" data-level="1.1.18.185"  data-name="Filter samples and genes with too many missing entries" title="on expression matrix data">
                    <a onclick="openHelp('WGCNA/filterData.html','1_1_18_185')" href="#"  id="1_1_18_185">Filter samples and genes with too many missing entries</a>
                </li>

                <li class="chapter" data-level="1.1.18.186"  data-name="Plot sample hierarchical cluster tree" title="on expression matrix data to detect outliers">
                    <a onclick="openHelp('WGCNA/sampleCluster.html','1_1_18_186')" href="#"  id="1_1_18_186">Plot sample hierarchical cluster tree</a>
                </li>

                <li class="chapter" data-level="1.1.18.187"  data-name="Analysis of scale free topology for multiple soft thresholding powers" title="to help the user pick an appropriate soft-thresholding power for network construction">
                    <a onclick="openHelp('WGCNA/pickSoftThreshold.html','1_1_18_187')" href="#"  id="1_1_18_187">Analysis of scale free topology for multiple soft thresholding powers</a>
                </li>

                <li class="chapter" data-level="1.1.18.188"  data-name="Analysis">
                    <a style='color:#52AB6C;'>Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.18.189"  data-name="WGCNA Analysis - network construction and module detection" title="on expression matrix data">
                    <a onclick="openHelp('WGCNA/wgcna.html','1_1_18_189')" href="#"  id="1_1_18_189">WGCNA Analysis - network construction and module detection</a>
                </li>

                <li class="chapter" data-level="1.1.18.190"  data-name="Visualization">
                    <a style='color:#52AB6C;'>Visualization</a>
                </li>

                <li class="chapter" data-level="1.1.18.191"  data-name="Plot Genes Topological Overlap Matrix Heatmap" title="combined with the corresponding hierarchical clustering dendrogram and module colors">
                    <a onclick="openHelp('WGCNA/plotHeatMap.html','1_1_18_191')" href="#"  id="1_1_18_191">Plot Genes Topological Overlap Matrix Heatmap</a>
                </li>

                <li class="chapter" data-level="1.1.18.192"  data-name="MDS Analysis and plot MDS" title="based on genes">
                    <a onclick="openHelp('WGCNA/mdsplot.html','1_1_18_192')" href="#"  id="1_1_18_192">MDS Analysis and plot MDS</a>
                </li>

                <li class="chapter" data-level="1.1.18.193"  data-name="About Modules">
                    <a style='color:#52AB6C;'>About Modules</a>
                </li>

                <li class="chapter" data-level="1.1.18.194"  data-name="Get Module Eigengenes" title="(1st principal component of the expression matrix of the corresponding module)">
                    <a onclick="openHelp('WGCNA/plotModuleGeneEx.html','1_1_18_194')" href="#"  id="1_1_18_194">Get Module Eigengenes</a>
                </li>

                <li class="chapter" data-level="1.1.18.195"  data-name="Plot module eigengene adjacency heatmap" title="()">
                    <a onclick="openHelp('WGCNA/plotModuleHeatmap.html','1_1_18_195')" href="#"  id="1_1_18_195">Plot module eigengene adjacency heatmap</a>
                </li>

                <li class="chapter" data-level="1.1.18.196"  data-name="Plot module cluster tree" title="based on ME correlation">
                    <a onclick="openHelp('WGCNA/moduleCluster.html','1_1_18_196')" href="#"  id="1_1_18_196">Plot module cluster tree</a>
                </li>

                <li class="chapter" data-level="1.1.18.197"  data-name="Phenotype Association">
                    <a style='color:#52AB6C;'>Phenotype Association</a>
                </li>

                <li class="chapter" data-level="1.1.18.198"  data-name="Module eigengene correlation analysis with phenotype" title="">
                    <a onclick="openHelp('WGCNA/PA.html','1_1_18_198')" href="#"  id="1_1_18_198">Module eigengene correlation analysis with phenotype</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.19"  data-name="NGS: Network Analysis">
            <b>NGS: Network Analysis</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.19.199"  data-name="Expression Pattern">
                    <a style='color:#52AB6C;'>Expression Pattern</a>
                </li>

                <li class="chapter" data-level="1.1.19.200"  data-name="Subcluster Expression Analysis" title="for fpkm/tpm matrix">
                    <a onclick="openHelp('rnaseq_toolkit/expressPattern.html','1_1_19_200')" href="#"  id="1_1_19_200">Subcluster Expression Analysis</a>
                </li>

                <li class="chapter" data-level="1.1.19.201"  data-name="Network">
                    <a style='color:#52AB6C;'>Network</a>
                </li>

                <li class="chapter" data-level="1.1.19.202"  data-name="Plot Genes subClusters Network" title="from subcluster expression analysis result">
                    <a onclick="openHelp('rnaseq_toolkit/expPattern_network.html','1_1_19_202')" href="#"  id="1_1_19_202">Plot Genes subClusters Network</a>
                </li>

                <li class="chapter" data-level="1.1.19.203"  data-name="Plot Gene Regulatory Network" title="according to genes correlation in samples">
                    <a onclick="openHelp('rnaseq_toolkit/gene_regula_network.html','1_1_19_203')" href="#"  id="1_1_19_203">Plot Gene Regulatory Network</a>
                </li>

                <li class="chapter" data-level="1.1.19.204"  data-name="For Cytoscape: Co-expression Network Analysis " title="">
                    <a onclick="openHelp('network/co-abund.html','1_1_19_204')" href="#"  id="1_1_19_204">For Cytoscape: Co-expression Network Analysis </a>
                </li>

                <li class="chapter" data-level="1.1.19.205"  data-name="For Cytoscape: retrieve pairs from Matrix" title="according to specific criterion">
                    <a onclick="openHelp('network/retri_pairs_in_matrix.html','1_1_19_205')" href="#"  id="1_1_19_205">For Cytoscape: retrieve pairs from Matrix</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.20"  data-name="data_stat">
            <b>data_stat</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.20.206"  data-name="univariate">
                    <a style='color:#52AB6C;'>univariate</a>
                </li>

                <li class="chapter" data-level="1.1.20.207"  data-name="Student T-test" title="between two independent or paired groups">
                    <a onclick="openHelp('diff/t_test.html','1_1_20_207')" href="#"  id="1_1_20_207">Student T-test</a>
                </li>

                <li class="chapter" data-level="1.1.20.208"  data-name="Wilcoxon-test " title="between two independent or paired groups">
                    <a onclick="openHelp('diff/wilcoxon_test.html','1_1_20_208')" href="#"  id="1_1_20_208">Wilcoxon-test </a>
                </li>

                <li class="chapter" data-level="1.1.20.209"  data-name="Analysis of variance" title="among more than two groups">
                    <a onclick="openHelp('diff/annova.html','1_1_20_209')" href="#"  id="1_1_20_209">Analysis of variance</a>
                </li>

                <li class="chapter" data-level="1.1.20.210"  data-name="Kruskal-Wallis rank sum test" title="among more than two groups">
                    <a onclick="openHelp('diff/kw_test.html','1_1_20_210')" href="#"  id="1_1_20_210">Kruskal-Wallis rank sum test</a>
                </li>

                <li class="chapter" data-level="1.1.20.211"  data-name="multivariate">
                    <a style='color:#52AB6C;'>multivariate</a>
                </li>

                <li class="chapter" data-level="1.1.20.212"  data-name="Support vector machine" title="()">
                    <a onclick="openHelp('diff/svm.html','1_1_20_212')" href="#"  id="1_1_20_212">Support vector machine</a>
                </li>

                <li class="chapter" data-level="1.1.20.213"  data-name="Random forest" title="()">
                    <a onclick="openHelp('diff/randomforeast.html','1_1_20_213')" href="#"  id="1_1_20_213">Random forest</a>
                </li>

                <li class="chapter" data-level="1.1.20.214"  data-name="oths">
                    <a style='color:#52AB6C;'>oths</a>
                </li>

                <li class="chapter" data-level="1.1.20.215"  data-name="logistic regression on two groups" title="()">
                    <a onclick="openHelp('diff/logistic_regression.html','1_1_20_215')" href="#"  id="1_1_20_215">logistic regression on two groups</a>
                </li>

                <li class="chapter" data-level="1.1.20.216"  data-name="Roc analysis" title="">
                    <a onclick="openHelp('roc_analysis/RocLine.html','1_1_20_216')" href="#"  id="1_1_20_216">Roc analysis</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.21"  data-name="Blast Tools">
            <b>Blast Tools</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.21.217"  data-name="Get Sequences from fasta file" title="given a seq IDs list file">
                    <a onclick="openHelp('misc/selSeq.html','1_1_21_217')" href="#"  id="1_1_21_217">Get Sequences from fasta file</a>
                </li>

                <li class="chapter" data-level="1.1.21.218"  data-name="Blast: pairwise alignment output">
                    <a style='color:#52AB6C;'>Blast: pairwise alignment output</a>
                </li>

                <li class="chapter" data-level="1.1.21.219"  data-name="NCBI BLAST+ blastn" title="Search nucleotide database with nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastn_wrapper.html','1_1_21_219')" href="#"  id="1_1_21_219">NCBI BLAST+ blastn</a>
                </li>

                <li class="chapter" data-level="1.1.21.220"  data-name="NCBI BLAST+ blastp" title="Search protein database with protein query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastp_wrapper.html','1_1_21_220')" href="#"  id="1_1_21_220">NCBI BLAST+ blastp</a>
                </li>

                <li class="chapter" data-level="1.1.21.221"  data-name="NCBI BLAST+ blastx" title="Search protein database with translated nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastx_wrapper.html','1_1_21_221')" href="#"  id="1_1_21_221">NCBI BLAST+ blastx</a>
                </li>

                <li class="chapter" data-level="1.1.21.222"  data-name="NCBI BLAST+ tblastn" title="Search translated nucleotide database with protein query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_tblastn_wrapper.html','1_1_21_222')" href="#"  id="1_1_21_222">NCBI BLAST+ tblastn</a>
                </li>

                <li class="chapter" data-level="1.1.21.223"  data-name="NCBI BLAST+ tblastx" title="Search translated nucleotide database with translated nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_tblastx_wrapper.html','1_1_21_223')" href="#"  id="1_1_21_223">NCBI BLAST+ tblastx</a>
                </li>

                <li class="chapter" data-level="1.1.21.224"  data-name="Blast: tabular output">
                    <a style='color:#52AB6C;'>Blast: tabular output</a>
                </li>

                <li class="chapter" data-level="1.1.21.225"  data-name="NCBI BLAST+ blastn(tabular)" title="Search nucleotide database with nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastn_wrapper_tab.html','1_1_21_225')" href="#"  id="1_1_21_225">NCBI BLAST+ blastn(tabular)</a>
                </li>

                <li class="chapter" data-level="1.1.21.226"  data-name="NCBI BLAST+ blastp(tabular)" title="Search protein database with protein query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastp_wrapper_tab.html','1_1_21_226')" href="#"  id="1_1_21_226">NCBI BLAST+ blastp(tabular)</a>
                </li>

                <li class="chapter" data-level="1.1.21.227"  data-name="NCBI BLAST+ blastx(tabular)" title="Search protein database with translated nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_blastx_wrapper_tab.html','1_1_21_227')" href="#"  id="1_1_21_227">NCBI BLAST+ blastx(tabular)</a>
                </li>

                <li class="chapter" data-level="1.1.21.228"  data-name="NCBI BLAST+ tblastn(tabular)" title="Search translated nucleotide database with protein query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_tblastn_wrapper_tab.html','1_1_21_228')" href="#"  id="1_1_21_228">NCBI BLAST+ tblastn(tabular)</a>
                </li>

                <li class="chapter" data-level="1.1.21.229"  data-name="NCBI BLAST+ tblastx(tabular)" title="Search translated nucleotide database with translated nucleotide query sequence(s)">
                    <a onclick="openHelp('misc/ncbi_tblastx_wrapper_tab.html','1_1_21_229')" href="#"  id="1_1_21_229">NCBI BLAST+ tblastx(tabular)</a>
                </li>

            </ul></li>
        <li class="chapter" data-level="1.1.22"  data-name="Image File Converters">
            <b>Image File Converters</b>
            <ul class="articles">

                <li class="chapter" data-level="1.1.22.230"  data-name="Convert PDF-to-PNG" title="()">
                    <a onclick="openHelp('image_tools/pdf2png.html','1_1_22_230')" href="#"  id="1_1_22_230">Convert PDF-to-PNG</a>
                </li>

                <li class="chapter" data-level="1.1.22.231"  data-name="Convert PDF-to-TIFF" title="()">
                    <a onclick="openHelp('image_tools/pdf2tiff.html','1_1_22_231')" href="#"  id="1_1_22_231">Convert PDF-to-TIFF</a>
                </li>

                <li class="chapter" data-level="1.1.22.232"  data-name="Convert PDF-to-JPG" title="()">
                    <a onclick="openHelp('image_tools/pdf2jpg.html','1_1_22_232')" href="#"  id="1_1_22_232">Convert PDF-to-JPG</a>
                </li>

            </ul>
        </li>

                </ul>
            </li>
            </ul>

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